package_references.txt

[[1]]
Paradis E, Schliep K (2019). “ape 5.0: an environment for modern phylogenetics
and evolutionary analyses in R.” _Bioinformatics_, *35*, 526-528.

[[2]]
McMurdie PJ, Paulson JN (2019). _biomformat: An interface package for the BIOM
file format_. https://github.com/joey711/biomformat/, http://biom-format.org/.

[[3]]
Pagès H, Aboyoun P, Gentleman R, DebRoy S (2019). _Biostrings: Efficient
manipulation of biological strings_. R package version 2.54.0.

[[4]]
Gu Z, Eils R, Schlesner M (2016). “Complex heatmaps reveal patterns and
correlations in multidimensional genomic data.” _Bioinformatics_.

[[5]]
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP (2016).
“DADA2: High-resolution sample inference from Illumina amplicon data.” _Nature
Methods_, *13*, 581-583. doi: 10.1038/nmeth.3869 (URL:
https://doi.org/10.1038/nmeth.3869).

[[6]]
Dowle M, Srinivasan A (2021). _data.table: Extension of `data.frame`_. R package
version 1.14.0, <URL: https://CRAN.R-project.org/package=data.table>.

[[7]]
Love MI, Huber W, Anders S (2014). “Moderated estimation of fold change and
dispersion for RNA-seq data with DESeq2.” _Genome Biology_, *15*, 550. doi:
10.1186/s13059-014-0550-8 (URL: https://doi.org/10.1186/s13059-014-0550-8).

[[8]]
Wickham H, Hester J, Chang W (2021). _devtools: Tools to Make Developing R
Packages Easier_. R package version 2.4.2, <URL:
https://CRAN.R-project.org/package=devtools>.

[[9]]
Wickham H, François R, Henry L, Müller K (2021). _dplyr: A Grammar of Data
Manipulation_. R package version 1.0.7, <URL:
https://CRAN.R-project.org/package=dplyr>.

[[10]]
Blighe K, Rana S, Lewis M (2019). _EnhancedVolcano: Publication-ready volcano
plots with enhanced colouring and labeling_. R package version 1.4.0, <URL:
https://github.com/kevinblighe/EnhancedVolcano>.

[[11]]
Larsson J (2021). _eulerr: Area-Proportional Euler and Venn Diagrams with
Ellipses_. R package version 6.1.1, <URL:
https://CRAN.R-project.org/package=eulerr>.

Larsson J, Gustafsson P (2018). “A Case Study in Fitting Area-Proportional Euler
Diagrams with Ellipses Using eulerr.” In _Proceedings of International Workshop
on Set Visualization and Reasoning_, volume 2116, 84-91. <URL:
https://cran.r-project.org/package=eulerr>.

[[12]]
Wickham H (2021). _forcats: Tools for Working with Categorical Variables
(Factors)_. R package version 0.5.1, <URL:
https://CRAN.R-project.org/package=forcats>.

[[13]]
Ogle DH, Doll JC, Wheeler P, Dinno A (2021). _FSA: Fisheries Stock Analysis_. R
package version 0.9.1, <URL: https://github.com/droglenc/FSA>.

[[14]]
Wickham H (2016). _ggplot2: Elegant Graphics for Data Analysis_. Springer-Verlag
New York. ISBN 978-3-319-24277-4, <URL: https://ggplot2.tidyverse.org>.

[[15]]
Wickham H (2016). _ggplot2: Elegant Graphics for Data Analysis_. Springer-Verlag
New York. ISBN 978-3-319-24277-4, <URL: https://ggplot2.tidyverse.org>.

[[16]]
Kassambara A (2020). _ggpubr: 'ggplot2' Based Publication Ready Plots_. R
package version 0.4.0, <URL: https://CRAN.R-project.org/package=ggpubr>.

[[17]]
Slowikowski K (2021). _ggrepel: Automatically Position Non-Overlapping Text
Labels with 'ggplot2'_. R package version 0.9.1, <URL:
https://CRAN.R-project.org/package=ggrepel>.

[[18]]
Gao C (2021). _ggVennDiagram: A 'ggplot2' Implement of Venn Diagram_. R package
version 1.1.4, <URL: https://CRAN.R-project.org/package=ggVennDiagram>.

[[19]]
Gao C (2021). _ggVennDiagram: A 'ggplot2' Implement of Venn Diagram_. R package
version 1.1.4, <URL: https://CRAN.R-project.org/package=ggVennDiagram>.

[[20]]
R Core Team (2020). _R: A Language and Environment for Statistical Computing_. R
Foundation for Statistical Computing, Vienna, Austria. <URL:
https://www.R-project.org/>.

[[21]]
Auguie B (2017). _gridExtra: Miscellaneous Functions for "Grid" Graphics_. R
package version 2.3, <URL: https://CRAN.R-project.org/package=gridExtra>.

[[22]]
Harrell Jr FE, Dupont wcfC, others. m (2021). _Hmisc: Harrell Miscellaneous_. R
package version 4.5-0, <URL: https://CRAN.R-project.org/package=Hmisc>.

[[23]]
Stansfield J, Dozmorov M (2019). _HMP2Data: 16s rRNA sequencing data from the
Human Microbiome Project 2_. R package version 1.0.0, <URL:
https://github.com/jstansfield0/HMP2Data>.

[[24]]
Csardi G, Nepusz T (2006). “The igraph software package for complex network
research.” _InterJournal_, *Complex Systems*, 1695. <URL: https://igraph.org>.

[[25]]
Bates D, Maechler M, Jagan M (2022). _Matrix: Sparse and Dense Matrix Classes
and Methods_. R package version 1.4-1, <URL:
https://CRAN.R-project.org/package=Matrix>.

[[26]]
Lahti L, Shetty S (2012-2019). “microbiome R package.”

[[27]]
Shetty S, Lahti L (2021). _microbiomeutilities: microbiomeutilities: Utilities
for Microbiome Analytics_. R package version 1.00.16.

[[28]]
Ramos M, Schiffer L, Re A, Azhar R, Basunia A, Cabrera CR, Chan T, Chapman P,
Davis S, Gomez-Cabrero D, Culhane AC, Haibe-Kains B, Hansen K, Kodali H, Louis
MS, Mer AS, Reister M, Morgan M, Carey V, Waldron L (2017). “Software For The
Integration Of Multi-Omics Experiments In Bioconductor.” _Cancer Research_,
*77(21); e39-42*.

[[29]]
McMurdie PJ, Holmes S (2013). “phyloseq: An R package for reproducible
interactive analysis and graphics of microbiome census data.” _PLoS ONE_,
*8*(4), e61217. <URL: http://dx.plos.org/10.1371/journal.pone.0061217>.

[[30]]
J L (2006). “Plotrix: a package in the red light district of R.” _R-News_,
*6*(4), 8-12.

[[31]]
PAUVERT C (2021). _psadd: Additions to phyloseq package for microbiome
analysis_. R package version 0.1.3.

[[32]]
Henry L, Wickham H (2020). _purrr: Functional Programming Tools_. R package
version 0.3.4, <URL: https://CRAN.R-project.org/package=purrr>.

[[33]]
Bisanz JE (2018). “qiime2R: Importing QIIME2 artifacts and associated data into
R sessions.” v0.99, <URL: https://github.com/jbisanz/qiime2R>.

[[34]]
Chen W, Simpson J, Levesque CA (2018). _RAM: R for Amplicon-Sequencing-Based
Microbial-Ecology_. R package version 1.2.1.7, <URL:
https://CRAN.R-project.org/package=RAM>.

Chen W, Simpson J, Levesque CA (2018). “RAM: R for Amplicon-Sequencing-Based
Microbial-Ecology.” R package version 1.2.1.7, <URL:
https://cran.r-project.org/package=RAM>.

[[35]]
Smith D (2021). _rbiom: Read/Write, Transform, and Summarize 'BIOM' Data_. R
package version 1.0.2.9025, <URL: https://cmmr.github.io/rbiom/index.html>.

[[36]]
Neuwirth E (2014). _RColorBrewer: ColorBrewer Palettes_. R package version
1.1-2, <URL: https://CRAN.R-project.org/package=RColorBrewer>.

[[37]]
Wickham H (2007). “Reshaping data with the reshape package.” _Journal of
Statistical Software_, *21*(12). <URL: http://www.jstatsoft.org/v21/i12/paper>.

[[38]]
Wickham H (2007). “Reshaping Data with the reshape Package.” _Journal of
Statistical Software_, *21*(12), 1-20. <URL: http://www.jstatsoft.org/v21/i12/>.

[[39]]
Wickham H, Seidel D (2020). _scales: Scale Functions for Visualization_. R
package version 1.1.1, <URL: https://CRAN.R-project.org/package=scales>.

[[40]]
Morgan M, Obenchain V, Hester J, Pagès H (2019). _SummarizedExperiment:
SummarizedExperiment container_. R package version 1.16.1.

[[41]]
Wickham H (2021). _tidyr: Tidy Messy Data_. R package version 1.1.3, <URL:
https://CRAN.R-project.org/package=tidyr>.

[[42]]
Wickham H, Averick M, Bryan J, Chang W, McGowan LD, François R, Grolemund G,
Hayes A, Henry L, Hester J, Kuhn M, Pedersen TL, Miller E, Bache SM, Müller K,
Ooms J, Robinson D, Seidel DP, Spinu V, Takahashi K, Vaughan D, Wilke C, Woo K,
Yutani H (2019). “Welcome to the tidyverse.” _Journal of Open Source Software_,
*4*(43), 1686. doi: 10.21105/joss.01686 (URL:
https://doi.org/10.21105/joss.01686).

[[43]]
Gehlenborg N (2019). _UpSetR: A More Scalable Alternative to Venn and Euler
Diagrams for Visualizing Intersecting Sets_. R package version 1.4.0, <URL:
https://CRAN.R-project.org/package=UpSetR>.

[[44]]
Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, Minchin PR,
O'Hara RB, Simpson GL, Solymos P, Stevens MHH, Szoecs E, Wagner H (2020).
_vegan: Community Ecology Package_. R package version 2.5-7, <URL:
https://CRAN.R-project.org/package=vegan>.


To cite R in publications use:

  R Core Team (2020). R: A language and environment for statistical computing. R
  Foundation for Statistical Computing, Vienna, Austria. URL
  https://www.R-project.org/.

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {R: A Language and Environment for Statistical Computing},
    author = {{R Core Team}},
    organization = {R Foundation for Statistical Computing},
    address = {Vienna, Austria},
    year = {2020},
    url = {https://www.R-project.org/},
  }

We have invested a lot of time and effort in creating R, please cite it when
using it for data analysis. See also ‘citation("pkgname")’ for citing R
packages.

R version 3.6.3 (2020-02-29)